Practical course on analysing the diversity of microbial eukaryotes in environments - MB160C87

• Title: Practical course on analysing the diversity of microbial eukaryotes in environments
• Czech title: Praktický kurz analýzy diverzity mikrobiálních eukaryot v prostředí
• Guaranteed by: Department of Parasitology (31-161)
• Faculty: Faculty of Science
• Actual: from 2024
• Semester: winter
• E-Credits: 4
• Examination process: winter s.:
• Hours per week, examination: winter s.:0/7, C [DS]
• Capacity: 6
• Min. number of students: 4
• 4EU+: yes
• Virtual mobility / capacity: yes / 4
• State of the course: taught
• Language: English
• Explanation: Will be held in Biocev in November 13.-21. See the Sylabus.
• Note: enabled for web enrollment
• Guarantor: doc. Mgr. Vladimír Hampl, Ph.D.
• Teacher(s): doc. Mgr. Vladimír Hampl, Ph.D.; Seda Mirzoyan, M.Sc.; Mgr. Jiří Novák; Mgr. Tomáš Pánek, Ph.D.

Annotation

This practical course focuses on the techniques of metabarcoding the eukaryotic diversity from environmental samples using short (V4 rRNA) and long (rRNA operon) amplicons. Students will learn the pipeline from the DNA isolation step to diversity estimation and data interpretation. Students will be grouped into pairs. Over the first three days (Wednesday to Friday), 36 marine samples (frozen cells on filters) from a spatial transect of the coast of northern France will be processed, three by each pair of students. Short and long amplicon libraries will be prepared and sequenced in-house on Illumina MiSeq and Oxford Nanopore MinION platforms over the weekend. During the following three days (Monday to Wednesday), the sequence data will be bioinformatically processed to estimate diversity, which will be compared between samples and sequencing technologies.

The course can accommodate 12 students and will be held at the research infrastructure BIOCEV from November 13th to 20th, 2024. The course will be conducted in English and taught by lecturers from the Departments of Parasitology (Vladimír Hampl, Jiří Novák) and Zoology (Ivan Čepička, Tomáš Pánek, Seda Mirzoyan) of Charles University, University of Warsaw (Anna Karnkowska, Michał Karlicki, Małgorzata Chwalińska), and Sorbonne University (Fabrice Not, Lucie Bittner).

Last update: Hampl Vladimír, doc. Mgr., Ph.D. (20.08.2024)

Requirements to the exam

Requirements for crediting are finalised protocols and presentation of the project results.

Last update: Hampl Vladimír, doc. Mgr., Ph.D. (20.08.2024)

Syllabus

SCHEDULE 2024

Wednesday, 13th of November

Introduction to the course plan, sample processing, and grouping of students
Hands-on activities:
    - DNA isolation
    - PCR for long amplicons
    - Setting up qPCR for short amplicons
    - Electrophoresis of long amplicons
    - Interpreting qPCR results
Summary of the day

Thursday, 14th of November

Lecture on Illumina amplicon sequencing
Hands-on activities:
    - Preparation of amplicon libraries for Illumina
    - Purification of the amplicon libraries
    - Measuring concentrations and quality
Summary of the day

Friday, 15th of November

Lecture on Nanopore amplicon sequencing
Hands-on activities:
    - Preparation of amplicon libraries
    - Loading the flow cell
Summary of the day
Social evening

Monday, 18th November

Lecture on raw data processing, OTU clustering, ASV and taxonomic annotations
Hands-on activities:
    - Data quality control and cleaning
    - Statistics, OTU clustering, ASV, and taxonomic annotation
    - Comparison of similarity versus phylogeny (Illumina versus Nanopore)
Summary of the day

Tuesday, 19th November

Lecture on diversity analyses
Hands-on activities:
    - Estimation of alpha-diversity
    - PCA on environmental parameters
    - Beta-diversity in our sequenced samples
    - Our samples in a broader context (MetaPR2)
Summary of the day

Wednesday, 20th November

Lecture on selected protist diversity studies from marine environments

Hands-on activities:
    - Finalizing data analyses, protocols, and preparation of presentations

Thursday, 21st of November

Lecture on selected protist diversity studies from freshwater environments
Student presentations of the data from the projects
Discussion
Departure

Last update: Hampl Vladimír, doc. Mgr., Ph.D. (20.08.2024)